include/gn/gnFilter.h

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00001 
00002 // File:            gnFilter.h
00003 // Purpose:         Filter for all Sequences
00004 // Description:     Filters sequences, translates, reverse complement, converts
00005 //                   additions, etc.
00006 // Changes:        
00007 // Version:         libGenome 0.5.1 
00008 // Author:          Aaron Darling 
00009 // Modified by:     
00010 // Copyright:       (c) Aaron Darling 
00011 // Licenses:        See COPYING file for details 
00013 #ifndef _gnSeqFilter_h_
00014 #define _gnSeqFilter_h_
00015 
00016 #include <string>
00017 #include "gn/gnClone.h"
00018 #include "gn/gnDefs.h"
00019 #include "gn/gnBaseFilter.h"
00020 
00021 const gnSeqC NO_REVCOMP_CHAR = 0;
00022 
00023 class GNDLLEXPORT gnFilter : public gnBaseFilter
00024 {
00025 public:
00026 
00027         static const gnFilter *alphabetCharacterFilter();
00028         static const gnFilter *numberCharacterFilter();
00029 
00030         static const gnFilter *proteinSeqFilter();
00031         static const gnFilter *basicDNASeqFilter();
00032         static const gnFilter *fullDNASeqFilter();
00033         static const gnFilter *basicRNASeqFilter();
00034         static const gnFilter *fullRNASeqFilter();
00035 
00036         static const gnFilter *DNAtoRNAFilter();
00037         static const gnFilter *RNAtoDNAFilter();
00038         static const gnFilter *DNAComplementFilter();
00039         static const gnFilter *RNAComplementFilter();
00040 
00041         enum gnFilterType{
00042                 alphabetCharacterFilterType,
00043                 numberCharacterFilterType,
00044 
00045                 proteinSeqFilterType,
00046                 basicDNASeqFilterType,
00047                 fullDNASeqFilterType,
00048                 basicRNASeqFilterType,
00049                 fullRNASeqFilterType,
00050 
00051                 DNAtoRNAFilterType,
00052                 RNAtoDNAFilterType,
00053                 DNAComplementFilterType,
00054                 RNAComplementFilterType
00055         };
00056 
00057 public:         
00058         gnFilter();
00065         gnFilter( const gnFilterType f_type );
00066         gnFilter( const gnSeqC defaultChar, const gnSeqC rdefaultChar );
00067         gnFilter( const gnFilter& sf );
00068         ~gnFilter();
00069         
00070         gnFilter* Clone() const;
00071 
00072         // gnSeqC 
00073         boolean IsValid( const gnSeqC ch ) const;
00074         gnSeqC MakeValid( const gnSeqC ch ) const;
00075         gnSeqC Filter( const gnSeqC ch ) const;
00076         // gnSeqC[]
00082         uint32 IsValid( const gnSeqC* seq, const uint32 len ) const;
00083         void MakeValid( gnSeqC* seq, const uint32 len ) const;
00084         void Filter( gnSeqC** seq, gnSeqI& len ) const;
00085         void ReverseFilter( gnSeqC** seq, gnSeqI& len ) const;
00086         // string
00087         uint32 IsValid( const string &seq ) const;
00088         void MakeValid( string &seq ) const;
00089         void Filter( string &seq ) const;
00090         void ReverseFilter( string &seq ) const;
00091 
00092         // Default gnSeqC
00093         void SetDefaultChar( const gnSeqC ch1, const gnSeqC ch2 );
00094         gnSeqC GetDefaultChar() const;
00095         gnSeqC GetRDefaultChar() const;
00096         // fill map
00097         void SetSingle( const gnSeqC ch );
00098         void SetPair( const gnSeqC ch1, const gnSeqC ch2 );
00099         boolean RemovePair( const gnSeqC ch );
00100         boolean RemoveSingle( const gnSeqC ch );
00101 
00102         // standard filters
00103 
00104 private:
00105         void CreateAlphabetCharacterFilter();
00106         void CreateNumberCharacterFilter();
00107 
00108         void CreateProteinFilter();
00109 
00110         void CreateBasicDNAFilter();
00111         void CreateFullDNAFilter();
00112 
00113         void CreateBasicRNAFilter();
00114         void CreateFullRNAFilter();
00115 
00116         void CreateDNAtoRNAFilter();
00117         void CreateRNAtoDNAFilter();
00118         void CreateDNAComplementFilter();
00119         void CreateRNAComplementFilter();
00120 
00121         gnSeqC m_pairArray[GNSEQC_MAX];
00122         gnSeqC m_defaultChar;
00123         gnSeqC m_rDefaultChar;
00124         
00125 };//class gnFilter
00126 
00127 inline
00128 gnFilter* gnFilter::Clone() const
00129 {
00130         return new gnFilter(*this);
00131 }
00132 
00133 // gnSeqC
00134 inline
00135 boolean gnFilter::IsValid( const gnSeqC ch ) const
00136 {
00137         return m_pairArray[(uint)ch] != NO_REVCOMP_CHAR;
00138 }
00139 inline
00140 gnSeqC gnFilter::MakeValid( const gnSeqC ch ) const
00141 {
00142         return (m_pairArray[(uint)ch] != NO_REVCOMP_CHAR? ch: m_defaultChar);
00143 }
00144 inline
00145 gnSeqC gnFilter::Filter( const gnSeqC ch ) const
00146 {
00147         
00148         return m_pairArray[(uint)ch] != NO_REVCOMP_CHAR ? m_pairArray[(uint)ch] : m_defaultChar;
00149 }
00150 // gnSeqC[]
00151 inline
00152 uint32 gnFilter::IsValid( const gnSeqC* seq, const uint32 len ) const
00153 {
00154         for( uint32 i=0; i < len ; ++i )
00155         {
00156                 if( !IsValid( seq[i] ) )
00157                         return i;
00158         }
00159         return len;
00160 }
00161 inline
00162 void gnFilter::MakeValid( gnSeqC* seq, const uint32 len ) const
00163 {
00164         for( uint32 i=0; i < len ; ++i )
00165         {
00166                 seq[i] = MakeValid( seq[i] );
00167         }
00168 }
00169 
00170 // string
00171 inline
00172 uint32 gnFilter::IsValid( const string &seq ) const
00173 {
00174         return IsValid( (gnSeqC*)seq.data(), seq.length() );
00175 }
00176 inline
00177 void gnFilter::MakeValid( string &seq ) const
00178 {
00179         MakeValid( (gnSeqC*)seq.data(), seq.length() );
00180 }
00181 
00182 // Default gnSeqC
00183 inline
00184 void gnFilter::SetDefaultChar( const gnSeqC ch1, const gnSeqC ch2 )
00185 {
00186         m_defaultChar = ch1;
00187         m_rDefaultChar = ch2;
00188 }
00189 inline
00190 gnSeqC gnFilter::GetDefaultChar() const
00191 {
00192         return m_defaultChar;
00193 }
00194 inline
00195 gnSeqC gnFilter::GetRDefaultChar() const
00196 {
00197         return m_rDefaultChar;
00198 }
00199 // fill map
00200 inline
00201 void gnFilter::SetSingle( const gnSeqC ch )
00202 {
00203         m_pairArray[(uint)ch] = ch;
00204 }
00205 inline
00206 void  gnFilter::SetPair( const gnSeqC ch1, const gnSeqC ch2 )
00207 {
00208         m_pairArray[(uint)ch1] = ch2;
00209 //      m_pairArray[(uint)ch2] = ch1;
00210 }
00211 inline
00212 boolean gnFilter::RemovePair( const gnSeqC ch )
00213 {
00214         m_pairArray[(uint)ch] = NO_REVCOMP_CHAR;
00215 //      m_pairArray[(uint)tmp] = NO_REVCOMP_CHAR;
00216         return true;
00217 }
00218 inline
00219 boolean gnFilter::RemoveSingle( const gnSeqC ch )
00220 {
00221         m_pairArray[(uint)ch] = NO_REVCOMP_CHAR;
00222         return true;    
00223 }
00224 
00225 #endif
00226         // __blSeqFilter_h__

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